R语言 R453Plus1Toolbox包 AVASet-class()函数中文帮助文档(中英文对照)

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AVASet-class(R453Plus1Toolbox)
AVASet-class()所属R语言包：R453Plus1Toolbox

                                        Class to contain Amplicon Variant Analyzer Output
                                         一类含有扩增变异分析仪输出

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Container to store data imported from a project of Roche's Amplicon Variant Analyzer Software. It stores all information into an extended version of the Biobase ExpressionSet.
从罗氏公司的扩增变异分析仪软件项目进口的数据存储容器。它存储到一个扩展版本，的BIOBASE ExpressionSet的所有信息。


类的对象----------Objects from the Class----------

Objects can be created by calls of the form AVASet(filename). While filename is the path of the project data (i.e. a directory  that contains the files and subdirectories "Amplicons/ProjectDef/ampliconsProject.txt", "Amplicons/Results/Variants/currentVariantDefs.txt",  "Amplicons/Results/Variants", "Amplicons/Results/Align").
创建对象可以通过检测的形式AVASet(filename)。虽然文件名是该项目的数据路径（即目录，其中包含的文件和子目录“扩增/ ProjectDef / ampliconsProject.txt”，“扩增/结果/变量/ currentVariantDefs.txt”，“扩增/结果/变种” ，“扩增/ /对齐”）。


插槽----------Slots----------




assayData: Object of class AssayData. Contains the number of reads and the total read depth for every variant and each
assayData类AssayData的对象。包含每一个变种，每个读取和读取的总深度




featureData: Object of class AnnotatedDataFrame. Contains information about the type, position and reference of each
featureData类AnnotatedDataFrame的对象。包含有关每个类型，位置和参考信息




phenoData: Object of class AnnotatedDataFrame. Contains the sample-IDs and name, annotation and group of the read data
phenoData类AnnotatedDataFrame的对象。包含样品ID和名称，注释和读取数据组




assayDataAmp: Object of class AssayData. Contains the number of reads for every amplicon and each sample in forward/reverse
assayDataAmp类AssayData的对象。在正向/反向每扩增和每个样本包含读取数




featureDataAmp: Object of class AnnotatedDataFrame. Contains the primer sequences, reference sequences and the coordinates
featureDataAmp类AnnotatedDataFrame的对象。包含的引物序列，参考序列和坐标




referenceSequences: Object of class AlignedRead. If additional alignment information were computed via
referenceSequences类AlignedRead的对象。通过计算，如果额外的对齐信息




variantFilterPerc: Object of class numeric. Contains a threshold to display only those variants, whose  coverage (in percent) in forward and reverse direction in at least one sample is higher than this filter value. See
variantFilterPerc类numeric的对象。包含一个阈值，以显示只有那些变种，其覆盖率（％）至少有一个样本是在正向和反向高于此过滤器的值。见




variantFilter: Object of class character. Contains a vector of variant names whose coverage (in percent) in forward and reverse direction in at least one sample is higher than the filter value in
variantFilter类character的对象。包含一个变种名称的覆盖率（％）至少有一个样本是在正向和反向高于筛选值的向量




dirs: Object of class character. Based on a directory given at instantiation of the object, it contains a vector of several
dirs类character的对象。基于对象的实例目录，它包含了几个向量




experimentData: Object of class MIAME. Contains details of the experiment.
experimentData类MIAME的对象。包含实验的细节。




annotation: Object of class character. Label associated with the annotation package used in the experiment.
annotation类character的对象。在实验中使用的注释包标签关联。




protocolData: Object of class annotatedDataFrame. Contains additional information about the samples.
protocolData类annotatedDataFrame的对象。包含有关样本的额外信息。




.__classVersion__: Object of class Versions. Remembers the R and R453Toolbox version numbers used to created the
.__classVersion__类Versions的对象。记得以创建使用R和R453Toolbox版本号


延伸----------Extends----------

Class eSet, directly. Class VersionedBiobase, by class "eSet", distance 2.  Class Versioned, by class "eSet", distance 3.
类eSet，直接。类VersionedBiobase，“ESET”级，距离为2。类Versioned，“ESET”级，距离3。


方法----------Methods----------




object[i,j]: Allows subsetting an AVASet object by features (i) and samples (j).
对象[I，J]：允许子集功能（I）和样品（J）AVASet对象。




assayDataAmp(object), assayDataAmp(object)<-value: Similar to assayData of the Biobase ExpressionSet, this function
assayDataAmp（对象），assayDataAmp（对象）<值：类似assayData：的BIOBASE ExpressionSet，这个功能的




fDataAmp(object): Similar to fData of the Biobase ExpressionSet, this function returns the amplicon feature data
对象）：fDataAmp（fDataBIOBASE ExpressionSet类似，这个函数返回的扩增功能数据




featureDataAmp(object), featureDataAmp(object)<-value: Similar to featureData of the Biobase ExpressionSet, this function
featureDataAmp（对象），featureDataAmp（对象）<值：类似featureData：的BIOBASE ExpressionSet，这个功能的




referenceSequences(object), referenceSequences(object)<-value: Returns/replaces the reference sequence slot.
referenceSequences（对象），referenceSequences（对象）<值：返回/替换的参考序列插槽。




alignShortReads(object, bsGenome): Retrieve the chromosomal positions of the amplicon
alignShortReads（对象bsGenome）的检索扩增的染色体位置




setVariantFilter(object): Sets the filter to display only those variants, whose coverage (in percent) in forward and reverse
setVariantFilter（对象）：设置过滤器显示只有那些变种，在前进的覆盖率（％）和扭转




getVariantPercentages(object) Computes the coverage for every variant over all reads (forward and/or reverse) and for each
getVariantPercentages（对象），计算每超过所有读取的变种（正向和/或反向），并为每个覆盖




annotateVariants(object): Annotates given genomic variants. See annotateVariants for details.
annotateVariants（对象）：注基因变种。看到annotateVariants详情。




htmlReport(object): Exports all (filtered) variant data into a html report. See htmlReport for details
htmlReport（对象）：出口（过滤）Variant数据到一个HTML报告。 htmlReport详情


作者（S）----------Author(s)----------


Christoph Bartenhagen



参见----------See Also----------

MapperSet-class, annotateVariants, alignShortReads, htmlReport, setVariantFilter, getVariantPercentages
MapperSet-class，annotateVariants，alignShortReads，htmlReport，setVariantFilter，getVariantPercentages


举例----------Examples----------



    # sum up class structure[总结班级结构]
    showClass("AVASet")

    # load an AVA dataset containing 6 samples, 4 amplicons and 259 variants[加载AVA的数据集，其中包含6个样品，4扩增和259变种]
    data(avaSetExample)
    avaSetExample

    # show contents of assay, feature and pheno data[分析，功能和苯酚数据显示的内容]
    head(assayData(avaSetExample)$variantForwCount)
    head(assayData(avaSetExample)$totalForwCount)
    head(assayData(avaSetExample)$variantRevCount)
    head(assayData(avaSetExample)$totalRevCount)
    head(fData(avaSetExample))
    pData(avaSetExample)
    assayDataAmp(avaSetExample)
    fDataAmp(avaSetExample)
    referenceSequences(avaSetExample)


转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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